The objective of this proposal is to explore the overall hypothesis that vaginal disease, namely bacterial vaginosis (BV), results from perturbations in the complex and multi-factorial interactions between the microbial components or microbiome and the host of the vaginal ecosystem. Specifically, we hypothesize: (1) BV is associated with a particular microbiome profile, (2) that the microbiome profile is shared across demographic groups, and (3) there is a corresponding, identifiable BV-associated metabolic state of the vaginal community. We propose to test these hypotheses by performing both 16S rRNA gene based and 454 metagenomic and transcriptomic sequencing and comparative analyses to determine the metabolic potential of the non-BV versus BV-associated vaginal microbiome. This knowledge will be important for identifying factors that contribute to and are predictive of the BV disease state. Specifically, we will (1) characterize the vaginal microbiome for a diverse population of women diagnosed with BV by 16S rRNA gene sequence analysis (2) identify specific genes associated with metabolic pathways unique to non-BV versus BV subjects by applying 454 sequencing to the metagenomic DNA and transcriptomic RNA isolated from vaginal samples obtained from non-BV and BV women (3) use a metagenomic approach to understand viral (both human viruses and bacteriophages) diversity and fungal diversity as it relates to BV, and (4) examine the temporal dynamics of the vaginal ecosystem by conducting longitudinal studies of defined populations. Molecular ecological characterization of the vaginal microbiome will provide objective analytical and biomolecular tools to assess women's health. These studies will correlate the vaginal microbiome and demographic background of the host to enable prediction of which women are at increased risk for vaginal infections, preterm birth, HIV and other sexually acquired diseases, and to provide opportunities for intervention.